mims-harvard/tooluniverse
57 skills
$npx skills add mims-harvard/tooluniverseSkillInstalls
setup-tooluniverseInstall and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands), or Python SDK (Coding API with 3 calling…tooluniverse-acmg-variant-classificationSystematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) for clinical significance.tooluniverse-admet-predictionComprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling for drug candidates.tooluniverse-adverse-event-detectionDetect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC).tooluniverse-adverse-outcome-pathwayMap environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-level toxicity.tooluniverse-aging-senescenceAging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug…tooluniverse-antibody-engineeringTherapeutic antibody engineering and optimization, lead-to-clinical-candidate.tooluniverse-antigravity-pluginInstall, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on Google Antigravity (AGY / Antigravity IDE / Antigravity 2.0).tooluniverse-binder-discoveryDiscover novel small-molecule binders for protein targets using structure-based and ligand-based screening.tooluniverse-biomedical-fact-lookupAnswer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory.tooluniverse-cancer-classificationTranslate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies.tooluniverse-cancer-genomics-tcgaTCGA/GDC cancer genomics analysis — cohort construction, clinical metadata retrieval, somatic mutation frequencies, survival analysis, and multi-omics…tooluniverse-cancer-variant-interpretationClinical interpretation of somatic cancer mutations for precision oncology.tooluniverse-cell-line-profilingCancer cell-line selection and profiling for experimental model choice.tooluniverse-chemical-compound-retrievalRetrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling.tooluniverse-chemical-safetyChemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experimental data, GHS/IARC hazard classification,…tooluniverse-chemical-sourcingFind commercial sources for chemical compounds — PubChem/ChEMBL identity resolution then vendor catalog search across ZINC, Enamine, eMolecules, Mcule.tooluniverse-claude-code-pluginInstall the ToolUniverse Claude Code plugin in one step — provides MCP server with 1000+ scientific tools, 120+ research skills, slash commands, hooks, and the…tooluniverse-clinical-data-integrationEnd-to-end drug safety review integrating FDA labels, FAERS adverse event reports, PRR/ROR disproportionality, pharmacogenomic biomarkers, clinical trial data,…tooluniverse-clinical-guidelinesSearch and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, USPSTF, IDSA, NIH consensus, ESMO/ESC/EASL…tooluniverse-clinical-risk-scoringCompute and interpret validated bedside clinical risk scores and pretest probabilities for an INDIVIDUAL patient — pick the right score for the scenario,…tooluniverse-clinical-trial-designStrategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory pathway)…tooluniverse-clinical-trial-matchingAI-driven patient-to-trial matching for precision oncology and rare-disease care.tooluniverse-comparative-genomicsCross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify…tooluniverse-computational-biophysicsSolve quantitative problems in biophysics — pharmacokinetics (PK volume of distribution, clearance, half-life), epidemiology (R0, attack rate), toxicology…tooluniverse-crispr-screen-analysisAnalyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritization, and pathway GSEA on screen output.tooluniverse-custom-toolAdd custom local tools to ToolUniverse alongside the 1000+ built-in tools.tooluniverse-data-integration-analysisIntegrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse databases (UniProt, GO, Reactome, ClinVar,…tooluniverse-data-wranglingUniversal data access patterns for downloading and parsing scientific data when ToolUniverse tools don't cover the source, only return metadata, or you need…tooluniverse-dataset-discoveryFind and evaluate research datasets for any scientific question.tooluniverse-diagnostic-test-evaluationDiagnostic test / biomarker accuracy — sensitivity, specificity, PPV, NPV, likelihood ratios, accuracy from a 2x2 table; ROC curve, AUC, and the optimal cutoff…tooluniverse-disease-researchGenerate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies, repurposing…tooluniverse-dose-responseDose-response / concentration-response curve fitting — IC50, EC50, Hill slope, Emax/Emin efficacy, and relative potency from paired concentration vs response…tooluniverse-drug-drug-interactionAssess drug-drug interactions — CYP metabolic interactions (substrate/inhibitor/inducer), transporter (P-gp, BCRP, OATP) effects, pharmacodynamic…tooluniverse-drug-mechanism-researchTrace drug mechanism of action — primary target → downstream signaling → pathway perturbation → tissue/organ effect → clinical outcome.tooluniverse-drug-regulatoryDrug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity,…tooluniverse-drug-repurposingIdentify drug repurposing candidates via target-based, compound-based, and disease-based strategies.tooluniverse-drug-researchComprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and…tooluniverse-drug-synergyDrug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic using the standard reference models (Bliss…tooluniverse-drug-target-validationQuantitative drug-target validation pipeline. Scores druggability, selectivity, safety profile, ADMET feasibility, and structural tractability with a composite…tooluniverse-ecology-biodiversityEcology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamics,…tooluniverse-electron-microscopySearch and analyze electron microscopy data — cryo-EM density maps (EMDB), fitted atomic models (PDB), raw micrograph datasets (EMPIAR), and cryo-electron…tooluniverse-enzyme-kineticsEnzyme kinetics — Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constant) from substrate-velocity data, plus…tooluniverse-epidemiological-analysisEnd-to-end observational epidemiology analysis — from research question (PECO Population/Exposure/Comparator/Outcome) to publication-ready statistical report.tooluniverse-epigenomicsGenomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility,…tooluniverse-epigenomics-chromatinHistone-modification ChIP-seq, ATAC-seq accessibility, chromatin state, and TF binding analysis from ENCODE, Roadmap Epigenomics, ChIP-Atlas.tooluniverse-expression-data-retrievalRetrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment.tooluniverse-fastq-qcFASTQ quality control and adapter/quality-trimming decisions with local NGS tools — run FastQC on raw reads, summarize a project with MultiQC, interpret…tooluniverse-functional-genomics-screensInterpret hits from CRISPR-KO/CRISPRi/shRNA screens by integrating DepMap essentiality, gnomAD constraint scores, pathway context (Reactome, STRING),…tooluniverse-gene-disease-associationGene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet.tooluniverse-gene-enrichmentGene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy,…tooluniverse-gene-regulatory-networksGene regulatory network analysis — TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, perturbation evidence…tooluniverse-gpcr-structural-pharmacologyGPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data, receptor-ligand binding analysis,…tooluniverse-gwas-drug-discoveryTransform GWAS signals into drug targets and repurposing opportunities.tooluniverse-gwas-finemappingStatistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP) and locus-to-gene scoring (Open Targets L2G).tooluniverse-gwas-snp-interpretationInterpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regulatory annotation, ClinVar pathogenicity,…tooluniverse-gwas-study-explorerCompare GWAS studies, perform meta-analyses across cohorts, and assess signal replication.